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(-) Description

Title :  DNA BOUND STRUCTURE OF THE N-TERMINAL DOMAIN OF ABRB
 
Authors :  J. Cavanagh, B. G. Bobay, D. M. Sullivan, R. J. Thompson
Date :  10 Mar 08  (Deposition) - 11 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D,E,F  (10x)
Keywords :  Abrb, Abrb8, Dna Bound, Transition State Regulator, Dna Binding Protein, Activator, Dna-Binding, Repressor, Sporulation, Transcription, Transcription Regulation, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Sullivan, B. G. Bobay, D. J. Kojetin, R. J. Thompson, M. Rance, M. A. Strauch, J. Cavanagh
Insights Into The Nature Of Dna Binding Of Abrb-Like Transcription Factors
Structure V. 16 1702 2008
PubMed-ID: 19000822  |  Reference-DOI: 10.1016/J.STR.2008.08.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSITION STATE REGULATORY PROTEIN ABRB
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector: PET24B
    Expression System Vector Type: VECTOR
    Fragment: SEQUENCE DATABASE RESIDUES 3-57
    Gene: ABRB, CPSX
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
 
Molecule 2 - DNA (25-MER)
    Chains: E
    Engineered: YES
    Mutation: YES
    Synthetic: YES
 
Molecule 3 - DNA (25-MER)
    Chains: F
    Engineered: YES
    Mutation: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2K1N)

(-) Sites  (0, 0)

(no "Site" information available for 2K1N)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:54 -C:54
2B:54 -D:54

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K1N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K1N)

(-) PROSITE Motifs  (1, 4)

NMR Structure (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SPOVT_ABRBPS51740 SpoVT-AbrB domain profile.ABRB_BACSU7-52
 
 
 		  4A:5-50
B:5-50
C:5-50
D:5-50

(-) Exons   (0, 0)

(no "Exon" information available for 2K1N)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:55
 aligned with ABRB_BACSU | P08874 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:55
                                    12        22        32        42        52     
            ABRB_BACSU    3 MKSTGIVRKVDELGRVVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMTCQ 57
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.........hhhhhhhhh.....eeeeeee..eeeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SPOVT_ABRB  PDB: A:5-50 UniProt: 7-52         ----- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  2k1n A  1 MKSTGIVRKVDELGRVVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMTCQ 55
                                    10        20        30        40        50     


Chain B from PDB  Type:PROTEIN  Length:55
 aligned with ABRB_BACSU | P08874 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:55
                                    12        22        32        42        52     
            ABRB_BACSU    3 MKSTGIVRKVDELGRVVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMTCQ 57
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.........hhhhhhhh......eeeeeee..eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SPOVT_ABRB  PDB: B:5-50 UniProt: 7-52         ----- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  2k1n B  1 MKSTGIVRKVDELGRVVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMTCQ 55
                                    10        20        30        40        50     


Chain C from PDB  Type:PROTEIN  Length:55
 aligned with ABRB_BACSU | P08874 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:55
                                    12        22        32        42        52     
            ABRB_BACSU    3 MKSTGIVRKVDELGRVVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMTCQ 57
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.........hhhhhhhhh.....eeeeeee..eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SPOVT_ABRB  PDB: C:5-50 UniProt: 7-52         ----- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  2k1n C  1 MKSTGIVRKVDELGRVVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMTCQ 55
                                    10        20        30        40        50     


Chain D from PDB  Type:PROTEIN  Length:55
 aligned with ABRB_BACSU | P08874 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:55
                                    12        22        32        42        52     
            ABRB_BACSU    3 MKSTGIVRKVDELGRVVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMTCQ 57
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
           Pfam domains (1) -------Antitoxin-MazE-2k1nD01 D:8-53                 -- Pfam domains (1)
           Pfam domains (2) -------Antitoxin-MazE-2k1nD02 D:8-53                 -- Pfam domains (2)
           Pfam domains (3) -------Antitoxin-MazE-2k1nD03 D:8-53                 -- Pfam domains (3)
           Pfam domains (4) -------Antitoxin-MazE-2k1nD04 D:8-53                 -- Pfam domains (4)
         Sec.struct. author ...eeeeee.........hhhhhhhhh.....eeeeeee..eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SPOVT_ABRB  PDB: D:5-50 UniProt: 7-52         ----- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  2k1n D  1 MKSTGIVRKVDELGRVVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMTCQ 55
                                    10        20        30        40        50     


Chain E from PDB  Type:DNA  Length:25
                                                        
                  2k1n E  1 ATGATTGACAATTATTGGAAACCTT 25
                                    10        20     


Chain F from PDB  Type:DNA  Length:25
                                                        
                  2k1n F  1 AAGGTTTCCAATAATTGTCAATCAT 25
                                    10        20
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2K1N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2K1N)

(-) Pfam Domains  (1, 4)

NMR Structure
(-)
Clan: AbrB (11)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A,B,C,D   (ABRB_BACSU | P08874)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0043937    regulation of sporulation    Any process that modulates the frequency, rate or extent of sporulation, the process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ABRB_BACSU | P08874: 1yfb 1ysf 1z0r 2mjg 2ro4

(-) Related Entries Specified in the PDB File

1z0r STRUCTURE OF THE N-TERMINAL DOMAIN OF ABRB